I will usually exterminate the populace of a newly conquered city as it gets rid of the culture penalty. Another thing is that exterminating the populace has a 2 fold effect it massacures a percentage of the population not everybody in the city, granted it's a high percentage 60-75% IIRC. And it lets your troops do extensive looting of the city, hence the large padding of your wallet. Enslaving the populace takes a smaller percentage of the population, 25-40%, and you only loot from the people you enslave. IMO massacuring the population gets rid of the cultural penalty because the praticers of the old culture are gone. Slaughtered in a night of the long knives-esque orgy of mass murder and mass thievery. The new people that migrate to the city are immerest in your culture and values and have no idea of what went on before, especially if your knock down the old temples.

Something else population growth in RTW comes from migration not reproduction. Other wise it makes no sense